Low base-substitution mutation rate and predominance of insertion-deletion events in the acidophilic bacterium Acidobacterium capsulatum


KÜÇÜKYILDIRIM ÇELİK S., Miller S. F. , Lynch M.

ECOLOGY AND EVOLUTION, vol.11, pp.17609-17614, 2021 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 11
  • Publication Date: 2021
  • Doi Number: 10.1002/ece3.8429
  • Journal Name: ECOLOGY AND EVOLUTION
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Agricultural & Environmental Science Database, BIOSIS, CAB Abstracts, Greenfile, Veterinary Science Database, Directory of Open Access Journals
  • Page Numbers: pp.17609-17614
  • Keywords: acidophile, mutation rate, mutation spectrum, PH, EVOLUTION, FRAMEWORK, DRIFT
  • Hacettepe University Affiliated: Yes

Abstract

Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0-8.0). In particular, the whole-genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome-wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation-accumulation experiment followed by whole-genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of similar to 2900 cell divisions yielded a base-substitution mutation rate of 1.22 x 10(-10) per site per generation or 4 x 10(-4) per genome per generation, which is significantly lower than the consensus value (2.5-4.6 x 10(-3)) of mesothermophilic (similar to 15-40 degrees C) and neutrophilic (pH 6-8) prokaryotic organisms. However, the insertion-deletion rate (0.43 x 10(-10) per site per generation) is high relative to the base-substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion-deletion rate may be balanced by a low base-substitution rate in A. capsulatum, with selection operating on the total mutation rate.